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Convert rows to columns based on condition


 
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Top Forums Shell Programming and Scripting Convert rows to columns based on condition
# 8  
Old 08-15-2013
Try to rename the file to txt, like file.bin -> file.txt

---------- Post updated at 14:46 ---------- Previous update was at 13:38 ----------

I do see several problems.
1. Lines becomes very long so they are wrapped on the screen. Should be no problem since field are tab separated.
2. Your data is not unique. I do store everything into array based on GN name, and since they are not unique this may mess things up.
Code:
GN   Name=HLA-A; Synonyms=HLAA;
RC   TISSUE=Blood;
CC   -!- FUNCTION: Involved in the presentation of foreign antigens to the
CC       immune system.
GN   Name=HLA-A; Synonyms=HLAA;
RC   TISSUE=Blood;
RC   TISSUE=Blood;
RC   TISSUE=Platelet;
CC   -!- FUNCTION: Involved in the presentation of foreign antigens to the
CC       immune system.

As you see here two section describing the same GN, but have different TISSUE
And as you see TISSUE do also have duplicate within one section.

To solve this I may make a script doing section by section, and not all in one array.
# 9  
Old 08-15-2013
Which is the GN name you are looking for? what about Synonyms?
Tissue is not identical, do you want only the uniqe ones or all of them?

--ahamed
# 10  
Old 08-16-2013
There are many isoforms so tissue field may not be identical even if they have same gene name. I want all (only if we consider gene names they appear to be duplicates but when we see other fields there would be some difference). synonyms are also needed sorry for not mentioning that earlier it would be better if it contains following fields
Code:
"GN","synonyms","TISSUE","FUNCTION"

# 11  
Old 08-16-2013
For the sample file you have provided, paste the expected output for first 3 set.

--ahamed
# 12  
Old 08-16-2013
sample output

I made it in .xls format so that the fields would be clearly seperated from each other. please see to it
# 13  
Old 08-16-2013
Try this
Code:
awk '
	/^GN/ {split($0,a,"[=;]");printf "\n%s|",a[2]}
	/^RC/ {split($0,a,"=");printf a[2];f=1}
	/^CC/ {if (f) {printf "|"};sub(/-!- FUNCTION:/,x);split($0,a,"  +");printf "%s ",a[2];f=0}
END {print ""}' uniprot_human_prts_with_tissue_fn

Every field is now separated by |, in TISSUE its separated by ;
What should we do with the Synonyms field? Print it, where?

3 first line:
Code:
YWHAB|Keratinocyte;Thymus;Skin;Colon carcinoma;Platelet;Melanoma;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negative regulator of osteogenesis. Blocks the nuclear translocation of the phosphorylated form (by AKT1) of SRPK2 and antagonizes its stimulatory effect on cyclin D1 expression resulting in blockage of neuronal apoptosis elicited by SRPK2.
YWHAE|Liver;Brain;Heart;Caudate nucleus, Heart, and Subthalamic nucleus;Placenta;Platelet;B-cell lymphoma;Histiocytic lymphoma;Brain, and Cajal-Retzius cell;Melanoma;Liver;Cervix carcinoma;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner.
YWHAH|Brain;Brain;Lymph;Keratinocyte;Platelet;Platelet;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negatively regulates the kinase activity of PDPK1.


EDIT: Here synonyms are printed behind original like: YWHAH-YWHA1
Code:
awk '
	/^GN/ {split($0,a,"[=;]");p=(a[4])?a[2]"-"a[4]:a[2];printf "\n%s|",p}
	/^RC/ {split($0,a,"=");printf a[2];f=1}
	/^CC/ {if (f) {printf "|"};sub(/-!- FUNCTION:/,x);split($0,a,"  +");printf "%s ",a[2];f=0}
END {print ""}' uniprot_human_prts_with_tissue_fn

Code:
YWHAB|Keratinocyte;Thymus;Skin;Colon carcinoma;Platelet;Melanoma;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negative regulator of osteogenesis. Blocks the nuclear translocation of the phosphorylated form (by AKT1) of SRPK2 and antagonizes its stimulatory effect on cyclin D1 expression resulting in blockage of neuronal apoptosis elicited by SRPK2.
YWHAE|Liver;Brain;Heart;Caudate nucleus, Heart, and Subthalamic nucleus;Placenta;Platelet;B-cell lymphoma;Histiocytic lymphoma;Brain, and Cajal-Retzius cell;Melanoma;Liver;Cervix carcinoma;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner.
YWHAH-YWHA1|Brain;Brain;Lymph;Keratinocyte;Platelet;Platelet;Leukemic T-cell;|Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner. Negatively regulates the kinase activity of PDPK1.


Last edited by Jotne; 08-16-2013 at 02:48 AM..
This User Gave Thanks to Jotne For This Post:
# 14  
Old 08-16-2013
Thats exactly what i needed

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